[R] retrieve most abundant species by sample unit

[Dave Roberts]

Graham,

It's relatively easily done, especially the first one.

Let's suppose your veg data frame is called veg

 > dom1 <- apply(veg,1,which.max)

returns a vector with the column number of the species with the highest 
abundance for each sample (if there are ties, it returns the first one).
If you're concerned about ties, you can check to see how many there are 
with

for (i in 1:nrow(veg)) print(sum(veg[i,]==dom1[i]))

There may be ways to eliminate the for loop, but this works

If you want the names of the species, rather than column number, you can do

 > names(veg)[dom1]

which will return the species names (assuming they are the column names 
of the data.frame).  Now to get the next most abundant species, zero out 
the dominant species and repeat

 > tmp <- veg
 > for (i in 1:nrow(veg)) tmp[i,dom1[i]] <- 0
 > dom2 <- apply(veg,1,which.max)

HTH Dave R

Graham Watt-Gremm wrote:
> Hi R-users:
> [R 2.2 on OSX 10.4.3]
> I have a (sparse) vegetation data frame with 500 rows (sampling  
> units) and 177 columns (plant species) where the data represent %  
> cover. I need to summarize the cover data by returning the names of  
> the most dominant and the second most dominant species per plot. I  
> reduced the data frame to omit cover below 5%; this is what it looks  
> like stacked. I have experimented with tapply(), by(), and some  
> functions mentioned in archived postings, but I haven't seen anything  
> that answers to this directly. Does anybody have any ideas?
> 
>       OBJECTID       PolygonID SpeciesCod AbundanceP
> 1       15006     ANT-CBG-rr1     Leymol    5.00000
> 3       15008     ANT-CBG-rr1     Ambcha    5.00000
> 5       15010      ANT-ESH-27     Atrpat   20.00000
> 6       15011      ANT-ESH-27     Ambcha   10.00000
> 11      15016      ANT-ESH-28     Salvir   20.00000
> 14      15019      ANT-ESH-28     Atrpat    5.00000
> 18      15023 ANT-POR-Rubarm5     Rubarm   60.00000
> 19      15024 ANT-POR-Rubarm5     Hedhel   40.00000
> 25      15030      ECO-CBG-A2     Griint    5.00000
> 27      15032      ECO-CBG-A2     Anngra    5.00000
> 38      15043      ECO-CBG-A4     Sperub   50.00000
> 
> Regards,
> Graham Watt-Gremm
> 
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-- 
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David W. Roberts                                     office 406-994-4548
Professor and Head                                      FAX 406-994-3190
Department of Ecology                         email droberts at montana.edu
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